Long working hours are known to have a negative effect on health. However, there is no clear evidence for a direct link between mental health and long working hours in the young adult populations. Therefore, we aimed to determine whether long working hours are associated with mental health in young adult workers. Data were collected from a 2012 follow-up survey of the Youth Panel 2007. A total of 3,332 young adult employees (aged 20 to 35) were enrolled in the study. We analyzed stress, depression, and suicidal thoughts by multivariate logistic regression analysis based on working hours (41 to 50, 51 to 60 and over 60 hours, compared to 31 to 40 hours per week), which was adjusted for sex, age, marriage status, region, and educational level. From the 3,332 young adult employees, about 60% of the workers worked more than 40 hours and 17% of the workers worked more than 50 hours per week. In a Chi-square test, stress level, depression, and suicidal thoughts increased with increasing working hours (p-value <0.001, 0.007, and 0.018, respectively). The multivariate logistic regression model showed that, compared to the 31 to 40 hours per week group, the adjusted odds ratios of the 41 to 50, 51 to 60, and over 60 hours per week groups for stress were 1.46(1.23-1.74), 2.25(1.79-2.83) and 2.55(1.72-3.77), respectively. A similar trend was shown in depression [odds ratios: 2.08(1.23-3.53), 2.79(1.44-5.39) and 4.09(1.59-10.55), respectively] and suicidal ideation [odds ratios: 1.98(0.95-4.10), 3.48(1.48-8.19) and 5.30(1.61-17.42), respectively]. We concluded that long working hours were associated with stress, depression, and suicidal ideation in young employees, aged 20 to 35.